The introduction of the Economic Cooperation Framework Agreement (ECFA) signed between China and Taiwan in 2010 has added a significantly important economic element to cross-strait relations. Little research has been done on cross-strait integration from an economic standpoint, and to analyze the potential for successful economic integration between the parties it is necessary to determine whether their political economies are compatible for integration. In this research comparative studies of the political economies of Taiwan and China are conducted with focuses on industrial orientation, market mechanisms, and the motivations driving major economic actors. This research focuses on Fujian and Guangdong, Taiwan’s closest economic partners on the mainland and the cornerstones of Beijing’s integration incentives, with a minor study conducted on Hong Kong-China integration due to similarities of economic integration mechanisms. This study uses models constructed by scholars on Chinese provincial protectionism and trade barriers to determine whether Taiwanese integration with the “Common China Market” will be mutually beneficial for the economies on both sides of the Taiwan Strait. Economic indicators, trade trends, and economic policy incentives indicate that integration under ECFA is amplifying trade asymmetries and is stalling real economic growth in Taiwan. Findings also show that trade liberalization has allowed major trade barrier and protectionism-creating phenomena that were once limited to the mainland to contribute to cross-strait competition regime among the economies studied. This research contributes to the fledgling body of academic research on cross-strait economic integration and its impact on the parties directly impacted by it. Implications of this study show that it would be beneficial for the speed of ECFA integration to be reigned in, and for Taiwan to use the trade agreement as a counter to pursue bilateral regional trade that can ensure its competitiveness.